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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('affyILM_1.65.0.tar.gz','quit-with-status'=TRUE)"
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── Installing affyILM ──────────────────────────────────────────────────────────
✔ Package installed successfully
── affyILM session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp8kbx2Y/file4c4846b74624e/affyILM
→ BiocVersion: 3.24
→ Package: affyILM
→ PackageVersion: 1.65.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/affyILM.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp8kbx2Y/file4c4846b74624e/affyILM
→ installDir: /tmp/Rtmp8kbx2Y/file4c4844c599848
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on affyILM ────────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
ℹ NOTE: Update R version dependency from 2.10.0 to 4.6.0
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
→ Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
ℹ NOTE: Consider adding these automatically suggested biocViews:
GeneExpression, ChipOnChip, GeneTarget
ℹ Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking if 'Package:' field matches directory / tarball...
* Checking for Version: field...
✖ ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (67%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
ℹ NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant,
consider adding the 'fnd' role to the list of authors.
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • affyILM.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • affyILM.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/affyILM.Rnw
* Checking package installation calls in R code...
* Checking for library/require of affyILM...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/affyilm_readIn.R (line 22, column 28)
    • ...
    • R/methods-ILM.R (line 298, column 55)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • affyilm_internal.R (line 7, column 18)
    • ...
    • methods-ILM.R (line 448, column 63)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/affyilm_readIn.R (line 8, column 9)
    • ...
    • cat() in R/methods-ILM.R (line 157, column 33)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/affyilm_internal.R (line 110, column 14)
    • ...
    • R/methods-ILM.R (line 271, column 39)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/methods-ILM.R (line 44, column 49)
    • R/methods-ILM.R (line 88, column 49)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 39 times:
    • T in R/affyilm_internal.R (line 129, column 102)
    • ...
    • F in R/methods-ILM.R (line 431, column 51)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 5
functions greater than 50 lines.
  The longest 5 functions are:
    • ilm() (R/affyilm.R): 227 lines
    • ...
    • validity() (R/AllClasses.R): 53 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/plotILM.Rd
    • man/plotIntens.Rd
* Checking package NEWS...
ℹ NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* Checking unit tests...
ℹ NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 111 lines (7%) are > 80 characters long.
  First few lines:
    • R/affyilm_internal.R#L47 se.temp2<-try(sqrt(rowSums(apply(data[p ...
    • ...
    • vignettes/affyILM.Rnw#L128 \item 4th and 5th column: \texttt{I0} in ...
ℹ NOTE: Consider 4 spaces instead of tabs; 867 lines (55%) contain tabs.
  First few lines:
    • R/affyilm_internal.R#L3 message("Computing hybridization free e ...
    • ...
    • man/ILM-class.Rd#L32 } ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 39 lines (2%) are not.
  First few lines:
    • R/methods-ILM.R#L350 if(nExprs>40) ...
    • ...
    • vignettes/affyILM.Rnw#L180 ...
ℹ See https://contributions.bioconductor.org/r-code.html
ℹ See styler package: https://cran.r-project.org/package=styler as described in
the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking for bioc-devel mailing list subscription...
ℹ NOTE: Cannot determine whether maintainer is subscribed to the Bioc-Devel
mailing list (requires admin credentials). Subscribe here:
https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
ℹ Maintainer is registered at support site.
ℹ Package is in the Support Site Watched Tags.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 3 WARNINGS | ℹ 18 NOTES
ℹ See the affyILM.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.